So I had to dig a little deeper, you can now run your Hybrid Worker Jobs as user, that you have stored in your Azure Automation credential store. Before Hybrid Worker jobs, would run as “LocalSystem” since that is the account the agent is running under. I don’t know, when this was added, but it has to be recently.
In order to set it up, you have to logon to the azure portal and go to
Automation Accounts -> -> Hybrid Worker Groups -> -> Settings -> Hybrid worker group settings